Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A9 F110 I1 R1 27 18.3 392680 99.5% 390716 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,371,220 C→T G95D (GGT→GAT)  rpsJ ← 30S ribosomal protein S10

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,371,2200CT100.0% 76.1 / NA 21G95D (GGT→GAT) rpsJ30S ribosomal protein S10
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (14/7);  total (14/7)

TACTACTGTTACAGGGATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATGCACGGCACGGATGA  >  USA300TCH1516_ALE/2371084‑2371352
                                                                                                                                        |                                                                                                                                    
tactacTGTTACAGGGATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGa                                                                                                                                  >  1:13441/1‑141 (MQ=255)
  ctactGTTACAGGGATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATg                                                                                                                                <  1:208570/141‑1 (MQ=255)
      tGTTACAGGGATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTaa                                                                                                                            >  1:289268/1‑141 (MQ=255)
      tGTTACAGGGATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTaa                                                                                                                            >  1:289244/1‑141 (MQ=255)
                                   cGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGttt                                                                                               >  1:171739/1‑141 (MQ=255)
                                      aTACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTg                                                                                            >  1:6862/1‑141 (MQ=255)
                                                cATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGtt                                                                                  <  1:131952/141‑1 (MQ=255)
                                                cATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGtt                                                                                  <  1:237128/141‑1 (MQ=255)
                                                   cccAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTAc                                                                               >  1:231794/1‑141 (MQ=255)
                                                                           tttGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTgtgtgt                                                       <  1:206779/141‑1 (MQ=255)
                                                                                              cctcctAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGCATTGttaa                                    >  1:99739/1‑139 (MQ=255)
                                                                                              cctcctAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCa                                    <  1:296975/141‑1 (MQ=255)
                                                                                              cctcctAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCa                                    >  1:113188/1‑141 (MQ=255)
                                                                                                   tAAAATTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTCAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGa                               >  1:375557/1‑141 (MQ=255)
                                                                                                       aTTGTCTATTATAATTTGATTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCt                           >  1:163076/1‑141 (MQ=255)
                                                                                                                         aTTTCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATgcacggca         <  1:88583/141‑1 (MQ=255)
                                                                                                                          tttCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGCTTAAGCGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATgcacggcac        >  1:106523/1‑141 (MQ=255)
                                                                                                                          tttCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATgcacggcac        >  1:385821/1‑141 (MQ=255)
                                                                                                                            tCGATGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATGcacggcacgg      <  1:377479/141‑1 (MQ=255)
                                                                                                                               aTGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATGCACGGCACGgatg   >  1:214400/1‑141 (MQ=255)
                                                                                                                                tGTCTACATCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATGCACGGCACGgatgt  >  1:2407/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                    
TACTACTGTTACAGGGATTAATTCACCGTTTTCTCCGAATACTTGTGTCATCCCAATTTTTCTTCCTAAGATTCCTTTGGTCATCGAAAGTCCACCTCCTAAAATTGTCTATTATAATTTGATTTCGATGTCTACACCAGATGGTAAGTTTAAGCCCATTAAAGCGTCAACTGTTTTTGGTGTTGGGTTTACAATATCGATTAAACGTTTGTGTGTACGTTGTTCGAATTGTTCACGTGAATCTTTATACTTATGCACGGCACGGATGA  >  USA300TCH1516_ALE/2371084‑2371352

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A